[gmx-users] Re: error in g_x2top

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 25 12:55:53 CEST 2011

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message there and ask that anything further 
be posted to the list.  See below for comments.

Zahra Kayani wrote:
> Dear, Dr.Lemkul
> command1:pdb2gmx -f shp2.pdb -o conf.gro it runs normally
> then for g_x2top, I tried these focefield :
> G53a5 GROMOS96 53a5 Forcefield (official distribution)
> oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> but for both of them this error was appeared, now what should I do?
> error: Could only find a forcefield type for 7351 out of 8397 atoms
> please,tell which forcefield can be helpful for me.

The .n2t files that come pre-packaged with these force fields are largely 
incomplete.  Further, g_x2top is designed for small molecules, and for anything 
complex, it may not be possible to define proper (non-conflicting) .n2t entries. 
  If you can get the topology via pdb2gmx, then you shouldn't have to do 
anything else.


> with regards
> Zahra


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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